Combine columns 2 and 3 to form the key of %duplicates.

use strict;
use warnings;

my %duplicates;
while (<DATA>) {
    chomp;
    my( $tracking_number, $description ) = split /,/, $_, 2;
    print $tracking_number, "\n" if exists $duplicates{$description};
    $duplicates{$description}++;
}
__DATA__
161248,/vol/filelist,CABINET
161200,/vol/filelist,INVENTORY
161400,/vol/filelist,INVENTORY
[download]

This worked great! Thanks Bill! I noticed the $_ and the 2 joined the columns as well.

It sounds like what you want to do is store the first column's value based on the most recent combined value of the second and third column's values. After you've read all of the input file, you want to dump out the results you've collected.

So, collect everything from the first file ..

my %data;
open my $FH2, '<', '/tmp/fileread' or
  die "unable to open input file: $!";
while(<$FH2>) {
  my @cols = split(/,/);
  $data{join(':',@cols[1,2])} = $cols[0];
}
close($FH2);
[download]

open my $FH6, '>', '/tmp/tst.txt' or
  die "unable to open output file: $!";
foreach my $key ( sort keys %data ) {
  my @keys = split(/:/,$key);
  print $FH6 join(',',$data{$key},@keys) . "\n";
}
close ( $FH6 );
[download]

If I understand what you are saying, you want to print when you get a match on both columns, but in your original code you are only keeping track of column 2. I would use a HASHES OF HASHES structure, with

open my $FH2, '<', '/tmp/fileread' or die "unable to open file 'file' 
+for reading : $!";
open my $FH6, '>', '/tmp/tst.txt' or die "unable to open file 'file' f
+or reading : $!";

my %duplicates;
while (<$FH2>) {
    chomp;
    my ($column_1, $column_2, $column_3) = split /,/;
    print {$FH6} "$column_1\n" if $duplicates{$column_2}{$column_3}++;
}
close $FH6;
close $FH2;
open my $fh, '<', '/tmp/tst.txt' or die "unable to open file 'file' fo
+r reading : $!";
while (my $line = <$fh>) {
print $line;
}
close $fh;
[download]